The collection of genes expressed by the microorganisms living in the human digestive tract. These include bacteria, archaea, fungi, and viruses. In humans, the gut microbiota has the largest numbers of bacteria and the greatest number of species compared to other areas of the body.

The relationship between gut microbiota and host is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship. Some human gut microorganisms benefit the host by fermenting dietary fiber into short-chain fatty acids (SCFAs), such as acetic acid and butyric acid, which are then absorbed by the host.

Your gut microbiota is the collection of microorganisms (bacteria, archaea, fungi, viruses) that live in your gastrointestinal tract. This is the bulk of your microbiome, containing tens of trillions of microorganisms and weighing about as much as your brain. In humans, the gut microbiota is established at one to two years after birth, and by that time the intestinal epithelium and the intestinal mucosal barrier that it secretes have co-developed in a way that is tolerant to, and even supportive of, the gut flora and that also provides a barrier to pathogenic organisms.

Your mother passes you your microbiome during birth. The process of receiving these foundational microbes is called seeding. It’s generally regarded to start at birth (though new research is starting to propose that microbial transmission could occur in the womb via the placenta), through the vaginal canal, skin-to-skin contact, and breastfeeding.

These first microbes colonize your gastrointestinal system and form the foundation of your immune system, serving as the instructors of what’s dangerous and what’s not. By the first few years of life, they stabilize into what is called the steady-state microbiome, resembling more or less what you have today.

The composition of human gut microbiota changes over time, when the diet changes, and as overall health changes.